1. System -> Battery & performance -> Manage app's battery usage -> Power Saving Modes -> select off
2. System -> Battery & performance -> Manage app's battery usage -> Saving Power in the background -> Choose Apps -> select Whatsapp and the options No restrictions and Allow
3. Setting the desired app into Autostart
4. Lock the app after you have opened for the first time

Thanks, but I've already tried all of these. The clean button will still close the apps. They will be restarted, yes, but for some accessibility apps (e.g. Universal Copy) this is not good enough.
Also not all apps have activities which can be pinned down.

So my issue still stands, if there are any more suggestions I'll be happy to hear.

For me, apps like WhatsApp, Facebook and other apps requiring Push Notifications work fine, even after clearing from task manager. But one thing irritates me, that is when I use VPN app.

In other ROMs, when I connect to VPN using an app and after connecting I clear it from task manager to prevent extra memory eating my battery and RAM. The VPN still works as even after clearing all tasks from Task Manager, the VPN symbol(a key icon) appears in my status bar.

But this is not the case with MIUI(all MIUIs including 8). Is there any way out? I hope my issue is conveyed clearly.

I solved this problem with the security app > cleaner > autostart. Added there the apps i want to be kept running in the background.
It is possible that this upgrade was added very recently because i only purchased this phone.

So do like this.
1. Do to Security app - then permissions - then autostart (here choose your apps). When this is done go to step 2.
2. Go to Settings - Additional settings - Battery - Manage apps battery usage - choose apps - choose your app and set it to NO RESTRICTIONS.
After those two actions your apps will always run in backround